The zoonotic disease Q fever is a caused by the obligate intracellular bacterium Coxiella burnetii. Coxiella burnetii has evolved strategies to survive in the hostile phagolysosomal environment. This agent is important for developing a comparative perspective on bacterial pathogenesis strategies. Most pathogens either do not survive extended periods in the environment or, like many Gram-positive agents, have evolved the ability to sporulate to survive long periods of dessication. Coxiella burnetii is a Gram-negative organisms that has developed a novel, non-sporulating strategy to survive in a non-replicative form for long periods. This property has lead to the consideration of this pathogen as a bio-warfare agent. Its stability in the environment presents a serious concern for officials responsible for planning a response to the illegitimate release of this agent. Elucidation of the complete genomic sequence would provide a major breakthrough in the design of therapeutic intervention and a unique perspective on its biology. We propose to sequence the 2.1 Mbp genome of Coxiella burnetii Nine Mile, phase I (RSA 493) because of its known virulence potential and subsequent potential for comparison with other isolate groups. The genome sequence will be accomplished by the whole genome random shotgun sequencing currently used at TIGR. Additionally, the genome will be annotated by computer techniques to identify all open reading frames (ORFs) and relate as many ORFs as possible to proteins of known function.